The standard genetic code can evolve from a two-letter GC code

The model of an iterated learning approach the origins of the genetic code inspired this related hypothesis about a simplified precursor to the standard four-letter genetic code, which will be released in Origins of Life and Evolution of Biospheres:

The standard genetic code can evolve from a two-letter GC code without information loss or costly reassignments

Alejandro Frank and Tom Froese

It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.


New paper on iterated learning at the origins of life

Jorge, Nathaniel and I have published an extension of our iterated learning approach to the origins of the genetic code in the Proceedings of the Artificial Life Conference 2018. We unexpectedly found that the most likely sequences in which amino acids get incorporated into the emerging genetic codes in our simulation model exhibit a remarkable overlap with the sequence predicted in the literature based on empirical considerations.

We will present this work at the ALIFE conference in Tokyo as part of the special session on “Hybrid Life: Approaches to integrate biological, artificial and cognitive systems”.

An iterated learning approach to the origins of the standard genetic code can help to explain its sequence of amino acid assignments

Tom Froese, Jorge I. Campos, and Nathaniel Virgo

Artificial life has been developing a behavior-based perspective on the origins of life, which emphasizes the adaptive potential of agent-environment interaction even at that initial stage. So far this perspective has been closely aligned to metabolism-first theories, while most researchers who study life’s origins tend to assign an essential role to RNA. An outstanding challenge is to show that a behavior-based perspective can also address open questions related to the genetic system. Accordingly, we have recently applied this perspective to one of science’s most fascinating mysteries: the origins of the standard genetic code. We modeled horizontal transfer of cellular components in a population of protocells using an iterated learning approach and found that it can account for the emergence of several key properties of the standard code. Here we further investigated the diachronic emergence of artificial codes and discovered that the model’s most frequent sequence of amino acid assignments overlaps significantly with the predictions in the literature. Our explorations of the factors that favor early incorporation into an emerging artificial code revealed two aspects: an amino acid’s relative probability of horizontal transfer, and its relative ease of discriminability in chemical space.

Figure 2

Illustration of the architecture of the genetic system of one of our hypothetical protocells.

Psychological study on chaos control

Dobri Dotov and I have published an extended abstract in the Proceedings of the Artificial Life Conference 2018 about the study that he realized at UNAM. We suggest that the results have implications for how we should think about how to stabilize the behavior of complex adaptive systems with which we can interact.

We will present this work at the ALIFE conference in Tokyo as part of the special session on “ALife and Society: Transcending the artificial-natural divide”.

Mutual synchronization and control between artificial chaotic system and human

Dobromir Dotov and Tom Froese

Dexterous assistive devices constitute one of the frontiers for hybrid human-machine systems. Manipulating unstable systems requires task-specific anticipatory dynamics. Learning this dynamics is more difficult when tasks, such as carrying liquid or riding a horse, produce unpredictable, irregular patterns of feedback and have hidden dimensions not projected as sensory feedback. We addressed the issue of coordination with complex systems producing irregular behaviour, with the assumption that mutual coordination allows for non-periodic processes to synchronize and in doing so to become regular. Chaos control gives formal expression to this: chaos can be stabilized onto periodic trajectories provided that the structure of the driving input takes into account the causal structure of the controlled system.

Can we learn chaos control in a sensorimotor task? Three groups practiced an auditory-motor synchronization task by matching their continuously sonified hand movements to sonified tutors: a sinusoid served as a Non-Interactive Predictable tutor (NIP), a chaotic system stood for a Non-Interactive Unpredictable tutor (NI-U), and the same system weakly driven by the participant’s movement stood for an Interactive Unpredictable tutor (I-U). We found that synchronization, dynamic similarity, and causal interaction increased with practice in I-U. Our findings have implications for current efforts to find more adequate ways of controlling complex adaptive systems.


Keynote at “Time, the Body, and the Other”

I will be a keynote speaker at the international conference on Time, the Body, and the Other: Phenomenological and Psychopathological Approaches, which will take place September 13-15, 2018, in Heidelberg.

The title of my contribution will be: “Integrating Phenomenology and Systems Theory: Time and the Other in Schizophrenia as a Case Study”


Talk at the Annual Meeting of the Society for American Archaeology

Next week I will present the latest installment of our model-based research into the social organization of ancient Teotihuacan at this year’s Annual Meeting of the Society for American Archaeology. Here is the title and abstract:

A network model of co-rulership and community ritual in Teotihuacan: From neighborhoods to districts

Tom Froese and Linda R. Manzanilla

Experts remain divided about the nature of the sociopolitical system of ancient Teotihuacan, which was one of the earliest and largest urban civilizations of the Americas. Excavations hoping to find compelling evidence of a powerful dynasty of rulers, such as a royal tomb, keep coming away empty-handed. However, the alternative possibility of a corporate or collective government, perhaps headed by a small number of co-rulers, also remains poorly understood. A third option is that the city’s collective government begun as a fully decentralized network of neighborhood representatives, but this kind of arrangement seems susceptible to the problems of cooperation and action coordination. Previously we used a computational model to show that in principle this latter worry is unfounded, as long as we assume that the network’s topology could be transformed via community rituals and was not strongly subdivided (Froese, Gershenson, and Manzanilla 2014). Here we extend this model to investigate whether centralized hierarchy could mitigate the negative effects of strong divisions. The new results reveal a peculiar synergy between hierarchy and community ritual in that only their combination improved the extent of coordination, which is consistent with portrayals of the elite as religious specialists serving the public.

A dynamical approach to the phenomenology of body memory

A special issue of the Journal of Consciousness Studies is in the final stages of preparation, following on from last year’s conference on the “Formation of Embodied Memory” in Heidelberg.

I teamed up with my old colleague Eduardo to put together the following article:

A dynamical approach to the phenomenology of body memory: Past interactions can shape present capacities without neuroplasticity

Tom Froese and Eduardo J. Izquierdo

Body memory comprises the acquired dispositions that constitute an individual’s present capacities and experiences. Phenomenological accounts of body memory describe its effects using dynamical metaphors: it is conceived of as curvatures in an agent-environment relational field, leading to attracting and repelling forces that shape ongoing sensorimotor interaction. This relational perspective stands in tension with traditional cognitive science, which conceives of the underlying basis of memory in representational-internal terms: it is the encoding and storing of informational content via structural changes inside the brain. We propose that this tension can be resolved by replacing the traditional approach with the dynamical approach to cognitive science. Specifically, we present three of our simulation models of embodied cognition that can help us to rethink the basis of several types of body memory. The upshot is that, at least in principle, there is no need to explain their basis in terms of content or to restrict their basis to neuroplasticity alone. Instead these models support the perspective developed by phenomenology: body memory is a relational property of a whole brain-body-environment system that emerges out of its history of interactions.

Jorge Campos receives 2018 ISAL Award for Outstanding Student Research

I am proud to announce that the International Society for Artificial Life (ISAL) has awarded the following conference paper, which was based on Jorge’s Master’s thesis, with the “2018 ISAL Award for Outstanding Student Research”:

Campos, J.I. & Froese, T. (2017). Referential communication as a collective property of a brain-body-environment-body-brain system: A minimal cognitive model. 2017 IEEE Symposium Series on Computational Intelligence (SSCI), Honolulu, HI: IEEE Press, pp. 863-870.

Out of the nominated papers this paper was chosen as the best in terms of its scientific rigor and clarity.

The award will be announced at the ALIFE 2018 conference in Tokyo this year. alife2018-logo-screengrab

New Spanish translation: Donde hay vida, hay mente

I was invited to contribute a chapter to the book Biocomplejidad edited by Moisés Villegas, Lorena Caballero and Eduardo Vizcaya. The book will come out online in open access format later this year.

The contribution is a Spanish translation of an article written by Kirchhoff and Froese (2017). Here it is:

Donde hay vida, hay mente: en apoyo a una tesis fuerte de la continuidad vida-mente

Michael D. Kirchhoff and Tom Froese

El presente texto considera cuestiones en torno a la continuidad y la discontinuidad entre la vida y la mente. Inicia examinando dichas cuestiones desde la perspectiva del principio de energía libre (PEL). El PEL se ha vuelto considerablemente influyente tanto en la neurociencia como en la ciencia cognitiva. Postula que los organismos actúan para conservarse a sí mismos en sus estados biológicos y cognitivos esperados, y que lo logran al minimizar su energía libre, dado que el promedio de energía libre a largo plazo es entropía. El texto, por lo tanto, argumenta que no existe una sola interpretación del PEL para pensar la relación entre la vida y la mente. Algunas formulaciones del PEL dan cuenta de lo que llamamos una perspectiva de independencia entre la vida y la mente. Una perspectiva de independencia es la perspectiva cognitivista del PEL, misma que depende del procesamiento de información con contenido semántico, y por ende, restringe el rango de sistemas capaces de exhibir mentalidad. Otras perspectivas de independencia ejemplifican lo que llamamos la demasiado generosa perspectiva no-cognitivista del PEL, que parecen ir en dirección opuesta: sugieren que la mentalidad se encuentra casi en cualquier lugar. El texto continúa argumentando que el PEL no-cognitivista y sus implicaciones para pensar la relación entre la vida y la mente puede ser útilmente delimitado por las recientes aproximaciones enactivas a la ciencia cognitiva. Concluimos que la versión más contundente de la relación vida-mente las considera fuertemente continuas, y esta continuidad se basa en conceptos particulares de vida (autopoiesis y adaptabilidad) y mente (básica y no-semántica).

A Role for Enhanced Functions of Sleep in Psychedelic Therapy?

This is the start of a fascinating new collaboration: we found that psilocybin can mitigate the negative effects of sleep disruption on memory consolidation in a dose-dependent manner!

I am particularly excited given that sleep disruption in this paradigm, the Morris Water Maze, has been proposed as surrogate for understanding pathological and aging-related loss of memory functions in humans!

Here is the paper:

A role for enhanced functions of sleep in psychedelic therapy?

Tom Froese, Iwin Leenen, and Tomas Palenicek

After a hiatus of several decades there has been a resurgence of studies into the therapeutic potential of serotonergic psychedelics. When administered in controlled settings, they have been reported to induce a wide variety of long-lasting positive psychological changes. However, the mechanisms by which psychedelics impart these long-lasting benefits remain poorly understood. Here we highlight one possibility that has remained underexplored: a beneficial interaction with the self-optimizing functions of sleep.

Explaining the origins of the genetic code without vertical descent

Here is the result of my two-month stay at the Earth-Life Science Institute (ELSI) of the Tokyo Institute of Technology, which was made possible by ELSI’s Origins Network. I quite like the implication that life could have been an inherently social phenomenon from its very origins!

Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent

Tom Froese, Jorge I. Campos, Kosuke Fujishima, Daisuke Kiga, and Nathaniel Virgo

Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. Woese’s solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells (“progenotes”), rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese’s conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone.

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